Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018087.1 Corchorus olitorius cultivar O-4 contig18120, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13641
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:379 original size:16 final size:16
Alignment explanation
Indices: 355--393 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
345 TTCTTGATCA
*
355 TTCGAGTTTTGGATTT
1 TTCGGGTTTTGGATTT
*
371 TTTGGGTTTTGGATTT
1 TTCGGGTTTTGGATTT
387 TTCGGGT
1 TTCGGGT
394 CTAGGACTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.05, G:0.31, T:0.56
Consensus pattern (16 bp):
TTCGGGTTTTGGATTT
Found at i:457 original size:24 final size:25
Alignment explanation
Indices: 424--480 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
414 GTCAGCCTTG
*
424 AATTT-TTTAATGT-TTAATTCTTA
1 AATTTATTTAATGTCTTAATTATTA
*
447 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGTCTTAATTATTA
472 AATTTATTT
1 AATTTATTT
481 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTAATGTCTTAATTATTA
Found at i:2241 original size:3 final size:3
Alignment explanation
Indices: 2221--2261 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
2211 CTTCTTCCTT
* * *
2221 TTA TTT TTA TTT TTA TTA TTA TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2262 TCTTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:3900 original size:25 final size:25
Alignment explanation
Indices: 3866--3917 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
3856 ATTCGTTCGC
3866 TATTTTATGGAGTAAATAAATATGG
1 TATTTTATGGAGTAAATAAATATGG
3891 TATTTTATGGAGTAAATAAATATGG
1 TATTTTATGGAGTAAATAAATATGG
3916 TA
1 TA
3918 CCACCAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (25 bp):
TATTTTATGGAGTAAATAAATATGG
Found at i:4411 original size:68 final size:68
Alignment explanation
Indices: 4322--4460 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
4312 AAAAGGATCT
*
4322 ACTGCTCTTTCAACTCGTCTATCTTGGTTTACAAGGTGATGATAAAATAAATTTTGCAACTTAAT
1 ACTGCTCTTTCAACTCGTCTATCTTGGTTTACAAGGTGATAATAAAATAAATTTTGCAACTTAAT
4387 TAG
66 TAG
*
4390 ACTGTTCTTTCAACTCGTCTATCTTGGTTTACAAGGTGATAATAAAATAAATTTTGCAACTTAAT
1 ACTGCTCTTTCAACTCGTCTATCTTGGTTTACAAGGTGATAATAAAATAAATTTTGCAACTTAAT
4455 TAG
66 TAG
4458 ACT
1 ACT
4461 AGGTACGTGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (68 bp):
ACTGCTCTTTCAACTCGTCTATCTTGGTTTACAAGGTGATAATAAAATAAATTTTGCAACTTAAT
TAG
Found at i:6039 original size:5 final size:5
Alignment explanation
Indices: 6029--6068 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
6019 TTATTTCTTA
*
6029 TGTTT TGTTT TGTTT TGTTT T-TTT T-TTT T-TTT TTTTT TGT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGT
6069 GCAGATGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
4 12 0.36
5 21 0.64
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (5 bp):
TGTTT
Found at i:8912 original size:2 final size:2
Alignment explanation
Indices: 8905--8944 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8895 AGGATGGAGG
8905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8945 GTAAAATCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9268 original size:20 final size:18
Alignment explanation
Indices: 9244--9280 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
9234 AATCGGTGCC
9244 ATATAATAAAAAAACAATA
1 ATATAAT-AAAAAACAATA
9263 AT-T-ATAAAAAACAATA
1 ATATAATAAAAAACAATA
9279 AT
1 AT
9281 TATAGGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.72
17 2 0.11
18 1 0.06
19 2 0.11
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
ATATAATAAAAAACAATA
Found at i:9273 original size:16 final size:16
Alignment explanation
Indices: 9252--9284 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
9242 CCATATAATA
9252 AAAAAACAATAATTAT
1 AAAAAACAATAATTAT
9268 AAAAAACAATAATTAT
1 AAAAAACAATAATTAT
9284 A
1 A
9285 GGAAGTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAACAATAATTAT
Done.